Diff of the two buildlogs: -- --- b1/build.log 2021-07-21 10:03:34.800888812 +0000 +++ b2/build.log 2021-07-21 09:38:17.705916946 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jul 20 21:38:32 -12 2021 -I: pbuilder-time-stamp: 1626860312 +I: Current time: Wed Jul 21 23:34:24 +14 2021 +I: pbuilder-time-stamp: 1626860064 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./roary_3.13.0+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.TuIQoOGA/trustedkeys.kbx': General error -gpgv: Signature made Fri Nov 8 01:51:49 2019 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.VO5vtLlW/trustedkeys.kbx': General error +gpgv: Signature made Sat Nov 9 03:51:49 2019 +14 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./roary_3.13.0+dfsg-1.dsc @@ -31,135 +31,169 @@ dpkg-source: info: applying new-bioperl-require.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/12665/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/27233/tmp/hooks/D01_modify_environment starting +debug: Running on virt64b. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/27233/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/27233/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='17bb0333bafe409d8ada44d2aaea676c' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='12665' - PS1='# ' - PS2='> ' + INVOCATION_ID=fff40c96f02f4ab0bf05b8ec23a7eead + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=27233 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.CVQbmZ5m3Y/pbuilderrc_VXBG --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.CVQbmZ5m3Y/b1 --logfile b1/build.log roary_3.13.0+dfsg-1.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.CVQbmZ5m3Y/pbuilderrc_J28q --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.CVQbmZ5m3Y/b2 --logfile b2/build.log --extrapackages usrmerge roary_3.13.0+dfsg-1.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux ff4a 5.10.0-8-armmp-lpae #1 SMP Debian 5.10.46-1 (2021-06-24) armv7l GNU/Linux + Linux i-capture-the-hostname 5.10.0-7-arm64 #1 SMP Debian 5.10.40-1 (2021-05-28) aarch64 GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Jun 21 14:26 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 Feb 7 02:38 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Feb 7 02:38 more - -rwsr-xr-x 1 root root 34400 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 9824 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 20 21:27 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Feb 7 02:38 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 Feb 7 02:38 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/12665/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Jun 22 16:26 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 Feb 8 04:38 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Feb 8 04:38 more + -rwsr-xr-x 1 root root 34400 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 9824 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 21 23:34 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 21 23:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Feb 8 04:38 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Feb 8 04:38 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/27233/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -558,7 +592,7 @@ Get: 301 http://deb.debian.org/debian bullseye/main armhf unzip armhf 6.0-26 [157 kB] Get: 302 http://deb.debian.org/debian bullseye/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 303 http://deb.debian.org/debian bullseye/main armhf r-base-core armhf 4.0.4-1 [24.8 MB] -Fetched 95.7 MB in 35s (2700 kB/s) +Fetched 95.7 MB in 24s (3996 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19398 files and directories currently installed.) @@ -1815,9 +1849,23 @@ Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). -0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +The following NEW packages will be installed: + usrmerge +0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. +Need to get 13.0 kB of archives. +After this operation, 43.0 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 13.0 kB in 0s (488 kB/s) +Selecting previously unselected package usrmerge. +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 33542 files and directories currently installed.) +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up usrmerge (25) ... +The system has been successfully converted. I: Building the package -I: Running cd /build/roary-3.13.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../roary_3.13.0+dfsg-1_source.changes +hostname: Name or service not known +I: Running cd /build/roary-3.13.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../roary_3.13.0+dfsg-1_source.changes dpkg-buildpackage: info: source package roary dpkg-buildpackage: info: source version 3.13.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -1849,92 +1897,92 @@ Writing Makefile for Bio::Roary Writing MYMETA.yml and MYMETA.json dh_auto_build -D .build/debian-build - cd .build/debian-build && make -j3 + cd .build/debian-build && make -j4 make[1]: Entering directory '/build/roary-3.13.0+dfsg/.build/debian-build' +cp lib/Bio/Roary/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.pm +cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm -cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm -cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm +cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm +cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm +cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm cp lib/Bio/Roary/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.pm -cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm cp lib/Bio/Roary/AssemblyStatistics.pm blib/lib/Bio/Roary/AssemblyStatistics.pm -cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm -cp lib/Bio/Roary/CommandLine/AssemblyStatistics.pm blib/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm -cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm -cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm -cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.pm -cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm -cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm +cp lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm blib/lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm +cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm cp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm +cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm +cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm +cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm +cp lib/Bio/Roary/CommandLine/AssemblyStatistics.pm blib/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm +cp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm +cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm +cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm +cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm +cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm +cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm +cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.pm +cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm -cp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm -cp lib/Bio/Roary/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.pm -cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm -cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm +cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm -cp lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm blib/lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm -cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm -cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm -cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm -cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm -cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm -cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm +cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.pm +cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm +cp lib/Bio/Roary/External/Fasttree.pm blib/lib/Bio/Roary/External/Fasttree.pm +cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm +cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm +cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm +cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm +cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.pm cp lib/Bio/Roary/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm -cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm -cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm +cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm -cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm -cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm +cp lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm -cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm -cp lib/Bio/Roary/External/IterativeCdhit.pm blib/lib/Bio/Roary/External/IterativeCdhit.pm -cp lib/Bio/Roary/Output/EMBLHeaderCommon.pm blib/lib/Bio/Roary/Output/EMBLHeaderCommon.pm -cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm -cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm cp lib/Bio/Roary/MergeMultifastaAlignments.pm blib/lib/Bio/Roary/MergeMultifastaAlignments.pm +cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm +cp lib/Bio/Roary/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm +cp lib/Bio/Roary/Output/EMBLHeaderCommon.pm blib/lib/Bio/Roary/Output/EMBLHeaderCommon.pm cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm -cp lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm -cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm -cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm -cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm +cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm -cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm -cp lib/Bio/Roary/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm -cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm -cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm -cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.pm -cp lib/Bio/Roary/External/Fasttree.pm blib/lib/Bio/Roary/External/Fasttree.pm +cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm +cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm +cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm +cp lib/Bio/Roary/External/IterativeCdhit.pm blib/lib/Bio/Roary/External/IterativeCdhit.pm cp lib/Bio/Roary/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm -cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm -cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm -cp lib/Bio/Roary/UniqueGenesPerSample.pm blib/lib/Bio/Roary/UniqueGenesPerSample.pm -cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm -cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm -cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm +cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm +cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm +cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm +cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm +cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm +cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm +cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm -cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm -cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm -cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.pm cp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm cp lib/Bio/Roary/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm +cp lib/Bio/Roary/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm +cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm +cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm +cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm +cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.pm +cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm -cp lib/Bio/Roary/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm -cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.pm -cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm -cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm +cp lib/Bio/Roary/UniqueGenesPerSample.pm blib/lib/Bio/Roary/UniqueGenesPerSample.pm +cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.pm cp bin/create_pan_genome blib/script/create_pan_genome cp bin/create_pan_genome_plots blib/script/create_pan_genome_plots -cp bin/extract_proteome_from_gff blib/script/extract_proteome_from_gff "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome_plots +cp bin/extract_proteome_from_gff blib/script/extract_proteome_from_gff "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/extract_proteome_from_gff cp bin/iterative_cdhit blib/script/iterative_cdhit "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/iterative_cdhit @@ -1953,8 +2001,8 @@ cp bin/query_pan_genome blib/script/query_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/query_pan_genome cp bin/roary blib/script/roary -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary cp bin/roary-create_pan_genome_plots.R blib/script/roary-create_pan_genome_plots.R +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-create_pan_genome_plots.R cp bin/roary-pan_genome_reorder_spreadsheet blib/script/roary-pan_genome_reorder_spreadsheet "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-pan_genome_reorder_spreadsheet @@ -1980,203 +2028,203 @@ dh_testroot dh_prep dh_auto_install -D .build/debian-build - cd .build/debian-build && make -j3 install DESTDIR=/build/roary-3.13.0\+dfsg/debian/roary AM_UPDATE_INFO_DIR=no PREFIX=/usr + cd .build/debian-build && make -j4 install DESTDIR=/build/roary-3.13.0\+dfsg/debian/roary AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/roary-3.13.0+dfsg/.build/debian-build' Manifying 16 pod documents Manifying 26 pod documents Manifying 28 pod documents Manifying 25 pod documents Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SpreadsheetRole.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SampleOrder.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PrepareInputFiles.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryBinaryFasta.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnalyseGroups.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReorderSpreadsheet.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SplitGroups.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/LookupGeneFiles.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnnotateGroups.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/BedFromGFFRole.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryBinaryFasta.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/OrderGenes.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReorderSpreadsheet.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PrepareInputFiles.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryClustering.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PostAnalysis.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/InflateClusters.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/MergeMultifastaAlignments.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFF.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SampleOrder.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AssemblyStatistics.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParseGFFAnnotationRole.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ChunkFastaFile.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ContigsToGeneIDsFromGFF.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CombinedProteome.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParallelAllAgainstAllBlast.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterFullClusters.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFF.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GeneNamesFromGFF.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFFs.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SequenceLengths.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/InflateClusters.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ClustersRole.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/BedFromGFFRole.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReformatInputGFFs.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/MergeMultifastaAlignments.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Exceptions.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupLabels.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFFs.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PostAnalysis.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/IterativeCdhit.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParseGFFAnnotationRole.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CombinedProteome.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/UniqueGenesPerSample.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GeneNamesFromGFF.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SequenceLengths.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupLabels.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnnotateGroups.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ContigsToGeneIDsFromGFF.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupStatistics.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ClustersRole.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SplitGroups.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PresenceAbsenceMatrix.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SortFasta.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParallelAllAgainstAllBlast.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/OrderGenes.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterUnknownsFromFasta.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/GeneAlignmentFromNucleotides.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Cdhit.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mcl.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Blastp.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Makeblastdb.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/PostAnalysis.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/CheckTools.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Prank.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/IterativeCdhit.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mafft.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Fasttree.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Exceptions.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SpreadsheetRole.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SortFasta.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PresenceAbsenceMatrix.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryPostAnalysis.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Common.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/QueryRoary.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/AssemblyStatistics.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryCoreAlignment.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Roary.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/IterativeCdhit.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/UniqueGenesPerSample.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Roary.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/UniqueGenesPerSample.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/QueryRoary.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Common.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/CreatePanGenome.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Role.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Parallel.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Role.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Local.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/QC/Report.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/DifferenceBetweenSets.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EMBLHeaderCommon.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastas.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastasNucleotide.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupMultifasta.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/NumberOfGroups.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/BlastIdentityFrequency.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaProtein.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaNucleotide.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Prank.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/GeneAlignmentFromNucleotides.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/PostAnalysis.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/IterativeCdhit.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Fasttree.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Blastp.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Cdhit.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Makeblastdb.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mafft.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mcl.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/CheckTools.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/QueryGroups.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EmblGroups.pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-unique_genes_per_sample.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/BlastIdentityFrequency.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaNucleotide.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/NumberOfGroups.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastas.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaProtein.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EMBLHeaderCommon.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/DifferenceBetweenSets.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupMultifasta.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastasNucleotide.pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/QC/Report.pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-query_pan_genome.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_assembly_statistics.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/parallel_all_against_all_blastp.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/protein_alignment_from_nucleotides.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/transfer_annotation_to_groups.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/extract_proteome_from_gff.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_core_alignment.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/iterative_cdhit.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/extract_proteome_from_gff.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-pan_genome_reorder_spreadsheet.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome_plots.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/query_pan_genome.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/transfer_annotation_to_groups.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_post_analysis.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/protein_alignment_from_nucleotides.1p Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_reorder_spreadsheet.1p -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GeneNamesFromGFF.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::QueryRoary.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnalyseGroups.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::QueryGroups.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Prank.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnnotateGroups.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mafft.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaNucleotide.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SortFasta.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupStatistics.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/parallel_all_against_all_blastp.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-unique_genes_per_sample.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome_plots.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_core_alignment.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/query_pan_genome.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_assembly_statistics.1p +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ExtractProteomeFromGff.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Makeblastdb.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ParallelAllAgainstAllBlast.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::EmblGroups.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFFs.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::TransferAnnotationToGroups.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryCoreAlignment.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Blastp.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SortFasta.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ChunkFastaFile.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReformatInputGFFs.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SpreadsheetRole.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AssemblyStatistics.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ParallelAllAgainstAllBlast.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Local.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastas.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ExtractProteomeFromGff.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::QC::Report.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ContigsToGeneIDsFromGFF.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::LookupGeneFiles.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::BedFromGFFRole.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ParseGFFAnnotationRole.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::IterativeCdhit.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Fasttree.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupStatistics.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GeneNamesFromGFF.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReformatInputGFFs.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnnotateGroups.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterUnknownsFromFasta.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PrepareInputFiles.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mcl.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupMultifasta.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Common.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CombinedProteome.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::IterativeCdhit.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupLabels.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaProtein.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ParseGFFAnnotationRole.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::CheckTools.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::UniqueGenesPerSample.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::LookupGeneFiles.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReorderSpreadsheet.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Prank.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::BlastIdentityFrequency.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Parallel.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::TransferAnnotationToGroups.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupMultifasta.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::IterativeCdhit.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SequenceLengths.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ClustersRole.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::GeneAlignmentFromNucleotides.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::CreatePanGenome.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SplitGroups.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PresenceAbsenceMatrix.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SpreadsheetRole.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::PostAnalysis.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractCoreGenesFromSpreadsheet.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Local.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::QueryGroups.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFF.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryReorderSpreadsheet.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::UniqueGenesPerSample.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ClustersRole.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Blastp.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::EMBLHeaderCommon.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SampleOrder.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaProtein.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::IterativeCdhit.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Roary.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterUnknownsFromFasta.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterFullClusters.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mafft.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::OrderGenes.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::AssemblyStatistics.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::UniqueGenesPerSample.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PrepareInputFiles.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::EmblGroups.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReorderSpreadsheet.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Role.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::DifferenceBetweenSets.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::BlastIdentityFrequency.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::IterativeCdhit.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::MergeMultifastaAlignments.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryPostAnalysis.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PostAnalysis.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Exceptions.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastasNucleotide.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::GeneAlignmentFromNucleotides.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Fasttree.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::CreatePanGenome.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SplitGroups.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::NumberOfGroups.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFF.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Common.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFFs.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::AssemblyStatistics.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SampleOrder.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AccessoryBinaryFasta.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PostAnalysis.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PresenceAbsenceMatrix.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AccessoryClustering.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterFullClusters.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AssemblyStatistics.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::QueryRoary.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryPostAnalysis.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::QC::Report.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnalyseGroups.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::GeneAlignmentFromNucleotides.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Role.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::MergeMultifastaAlignments.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaNucleotide.3pm +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastas.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::InflateClusters.3pm Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Cdhit.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupLabels.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::GeneAlignmentFromNucleotides.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ContigsToGeneIDsFromGFF.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Makeblastdb.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::IterativeCdhit.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CombinedProteome.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::PostAnalysis.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::CheckTools.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AccessoryClustering.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Exceptions.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractCoreGenesFromSpreadsheet.3pm -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_reorder_spreadsheet -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-pan_genome_reorder_spreadsheet -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome_plots -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-create_pan_genome_plots.R -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-unique_genes_per_sample -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/transfer_annotation_to_groups -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_assembly_statistics -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-query_pan_genome -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/query_pan_genome -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_post_analysis -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/extract_proteome_from_gff -Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/protein_alignment_from_nucleotides Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/iterative_cdhit +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-create_pan_genome_plots.R Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_core_alignment +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome_plots +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-pan_genome_reorder_spreadsheet +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_reorder_spreadsheet +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/protein_alignment_from_nucleotides +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-query_pan_genome +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/extract_proteome_from_gff Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/parallel_all_against_all_blastp +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_post_analysis +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_assembly_statistics +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/transfer_annotation_to_groups +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/query_pan_genome +Installing /build/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-unique_genes_per_sample make[1]: Leaving directory '/build/roary-3.13.0+dfsg/.build/debian-build' dh_installdocs dh_installchangelogs @@ -2200,12 +2248,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/27233/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/27233/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/12665 and its subdirectories -I: Current time: Tue Jul 20 22:03:30 -12 2021 -I: pbuilder-time-stamp: 1626861810 +I: removing directory /srv/workspace/pbuilder/27233 and its subdirectories +I: Current time: Wed Jul 21 23:38:14 +14 2021 +I: pbuilder-time-stamp: 1626860294